Locus 7342

Sequence ID	2L_DroMel_CAF1
Location	20,482,620 – 20,482,859
Length	239
Max. P	0.682920

overview

Window 8

Location	20,482,620 – 20,482,740
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.08
Mean single sequence MFE	-30.30
Consensus MFE	-24.64
Energy contribution	-25.52
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-1.33
Structure conservation index	0.81
SVM decision value	-0.01
SVM RNA-class probability	0.530631
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20482620 120 - 22407834
UUUCCGCUGCACCUUAUAGAAAAAGUUAUCCAUAGUAGACAUUGUUCUAUUUAUACAAAAUAUAUAUUCCGAUUUGGUGGUGAUAUGAUGUGUGUGAACUCUGCAAUCGGUCGGUGCAGU
.....((((((((((((.((........)).))))..((((((((....((((((((...(((((...(((......)))..)))))...))))))))....)))))..))))))))))) ( -30.90)
>DroSec_CAF1 35543 120 - 1
UUUCCGCUGCACCUUAUAGAAAAAGUCAUCCAUUGUAGCCAUGGUUCUAUUUAUACAAAAUAUAUAUUCCUGUUUGGUGGUGAUAUGACGUGUGUGAACUCUGCAAUCGGUCGGUGCAGU
.....((((((((.....((.....))..(((((((((....(((((....(((((...((((.....((.....)).....))))...))))).)))))))))))).))..)))))))) ( -32.10)
>DroSim_CAF1 39366 120 - 1
UUUCCGCUGCACCUUAUAGAAAAAGUCAUCCAUUGUAGCCAUGGUUCUAUUUAUACAAAAUAUAUAUUCCUGUUUGGUGGUGAUAUGACGUGUGUGAACUCUGCAAUCGGUCGGUGCAGU
.....((((((((.....((.....))..(((((((((....(((((....(((((...((((.....((.....)).....))))...))))).)))))))))))).))..)))))))) ( -32.10)
>DroEre_CAF1 37942 119 - 1
UUUCCGCUGCACCUUGUGGAAAUAAUCAUCCAUUGUAGCCAUUGUUCUAUUUAUACA-AAUGUAUAUUCCUAUUCGGUGGUGAUAAGUCGUGUGUGAACUCUGCAAUCGGUCAGUGCAGU
.....(((((((...(((((........)))))....((((((((....((((((((-....(((...((........))..))).....))))))))....))))).)))..))))))) ( -30.60)
>DroYak_CAF1 35294 119 - 1
UUUCCGCUGCACCUUAUGGAAGAAAUCAUCCAUUGUAGCCAUUGUUCUAUUUAAAGA-AAUAUAUAUUCCAAUUUGGUGGUGAUAUGACGUGUGUGAACUCUGCAAUCGGUCAGUGCAGU
.....(((((((....((((.(....).))))((((((.....(((((((((....)-))))(((((((((......))).))))))........)))).)))))).......))))))) ( -25.80)
>consensus
UUUCCGCUGCACCUUAUAGAAAAAGUCAUCCAUUGUAGCCAUUGUUCUAUUUAUACAAAAUAUAUAUUCCUAUUUGGUGGUGAUAUGACGUGUGUGAACUCUGCAAUCGGUCGGUGCAGU
.....((((((((.....((.....))..(((((((((.....((((....(((((...((((.....((.....)).....))))...))))).)))).))))))).))..)))))))) (-24.64 = -25.52 +   0.88)

alignment

secondary structure

dotplot

Window 9

Location	20,482,740 – 20,482,859
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.03
Mean single sequence MFE	-27.96
Consensus MFE	-21.67
Energy contribution	-20.91
Covariance contribution	-0.76
Combinations/Pair	1.22
Mean z-score	-1.63
Structure conservation index	0.77
SVM decision value	0.31
SVM RNA-class probability	0.682920
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20482740 119 + 22407834
CAUCCCACCAUUCUGGACGACUUGCGAGCAGUUUUCAAAAACUCGCAAAGUGAUUCUCCACAGCGUUCAAUAACUCUAUCCCAAAUACGUGGUAAGAAUUCCGUUUUUUCA-UCCAGGUA
...........((((((.((.(((((((.............))))))).(..(((((..((.((((....................)))).)).)))))..)......)).-)))))).. ( -24.47)
>DroSec_CAF1 35663 119 + 1
CAUCCCAACAUUCUGGACGACUUGCGAGCAGUUUUCAAAAACUCGCAAAGCGAUUCGCCGCAUCGUUCAAUAACUCUAUCCCAAAUACGUGGUAAGAAUCCGCUCUUUUCA-UCCAGGUA
...........((((((.((.(((((((.............)))))))(((((((((((((...........................)))))..)))).))))....)).-)))))).. ( -27.75)
>DroSim_CAF1 39486 119 + 1
CAUCCCACCAUUCUGGACGACUUGCGAGCAGUUUUCAAAAACUCGCAAAGCGAUUCGCCGCAUCGUUCAAUAACUCUAUCCCAAAUACGUGGUAAGAAUCCGCUCUUUUCA-UCCAGGUA
...........((((((.((.(((((((.............)))))))(((((((((((((...........................)))))..)))).))))....)).-)))))).. ( -27.75)
>DroEre_CAF1 38061 120 + 1
CAUCCGACCAUUCUGGACGACUUGCGAGAAGUUUUCAAAAACUCGCAGAGCGAUUCACCACAGCGUUCCAUAACGCUAUCCCAAAUACGUGGUAAGAACCCCGAACUGUUGUUCCAGGUA
..((..(((((..(((.((..(((((((.............)))))))..)).........((((((....))))))...))).....)))))..))(((..((((....))))..))). ( -31.32)
>DroYak_CAF1 35413 119 + 1
CAUCCCACCAUUCUGGAUGACUUGCGAGCAGUUUUUAAAAACUCGCAGAGCGAUUCACCACAGCGUUCAAUAACUCUGUCCCAAAUACGUGGUAGGAACAUCGAAUUUUUA-UCCAGGUA
...........(((((((((.(((((((.............)))))))..((((...((((((.(((....))).)))).(((......)))..))...)))).....)))-)))))).. ( -28.52)
>consensus
CAUCCCACCAUUCUGGACGACUUGCGAGCAGUUUUCAAAAACUCGCAAAGCGAUUCACCACAGCGUUCAAUAACUCUAUCCCAAAUACGUGGUAAGAAUCCCGUAUUUUCA_UCCAGGUA
...........((((((((..(((((((.............)))))))..)).((((((((...........................)))))..)))..............)))))).. (-21.67 = -20.91 +  -0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:11 2006